Fri, 31 Jul 2020

Package genieclust updated to version 0.9.4 with previous version 0.9.3 dated 2020-07-30

Title: The Genie++ Hierarchical Clustering Algorithm with Noise Points Detection
Description: A retake on the Genie algorithm - a robust hierarchical clustering method (Gagolewski, Bartoszuk, Cena, 2016 <DOI:10.1016/j.ins.2016.05.003>). Now faster and more memory efficient; determining the whole hierarchy for datasets of 10M points in low dimensional Euclidean spaces or 100K points in high-dimensional ones takes only 1-2 minutes. Allows clustering with respect to mutual reachability distances so that it can act as a noise point detector or a robustified version of 'HDBSCAN*' (that is able to detect a predefined number of clusters and hence it does not dependent on the somewhat fragile 'eps' parameter). The package also features an implementation of economic inequity indices (the Gini, Bonferroni index) and external cluster validity measures (partition similarity scores; e.g., the adjusted Rand, Fowlkes-Mallows, adjusted mutual information, pair sets index). See also the 'Python' version of 'genieclust' available on 'PyPI', which supports sparse data, more metrics, and even larger datasets.
Author: Marek Gagolewski [aut, cre, cph] (<https://orcid.org/0000-0003-0637-6028>), Maciej Bartoszuk [ctb], Anna Cena [ctb], Peter M. Larsen [ctb]
Maintainer: Marek Gagolewski <marek@gagolewski.com>

Diff between genieclust versions 0.9.3 dated 2020-07-30 and 0.9.4 dated 2020-07-31

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New package assertive with initial version 0.3-6
Package: assertive
Type: Package
Title: Readable Check Functions to Ensure Code Integrity
Version: 0.3-6
Date: 2020-07-30
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Authors@R: person("Richard", "Cotton", role = c("aut", "cre"), email = "richierocks@gmail.com")
Description: Lots of predicates (is_* functions) to check the state of your variables, and assertions (assert_* functions) to throw errors if they aren't in the right form.
URL: https://bitbucket.org/richierocks/assertive
BugReports: https://bitbucket.org/richierocks/assertive/issues
Depends: R (>= 3.0.0)
Imports: assertive.base (>= 0.0-4), assertive.properties (>= 0.0-2), assertive.types (>= 0.0-2), assertive.numbers, assertive.strings, assertive.datetimes, assertive.files, assertive.sets (>= 0.0-2), assertive.matrices, assertive.models, assertive.data, assertive.data.uk, assertive.data.us, assertive.reflection (>= 0.0-2), assertive.code, knitr
Suggests: testthat, markdown
License: GPL (>= 3)
LazyLoad: yes
LazyData: yes
VignetteBuilder: knitr
Acknowledgments: Development of this package was partially funded by the Proteomics Core at Weill Cornell Medicine - Qatar <http://qatar-weill.cornell.edu>. The Core is supported by 'Biomedical Research Program' funds, a program funded by Qatar Foundation.
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-07-31 18:29:39 UTC; richierocks
Repository: CRAN
Date/Publication: 2020-08-01 01:00:02 UTC

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New package xlsimple with initial version 1.0.5
Package: xlsimple
Type: Package
Title: 'XLConnect' Wrapper
Description: Provides a simple wrapper for some 'XLConnect' functions. 'XLConnect' is a package that allows for reading, writing, and manipulating 'Microsoft Excel' files. This package, 'xlsimple', adds some documentation and pre-defined formatting to the outputted 'Excel' file. Individual sheets can include a description on the first row to remind user what is in the data set. Auto filters and freeze rows are turned on. A brief readme file is created that provides a summary listing of the created sheets and, where provided, the description.
Authors@R: c(person("Jon", "Harcum", role="aut"), person("Erik W.", "Leppo", email="Erik.Leppo@tetratech.com",role=c("aut","cre")))
Maintainer: Erik W. Leppo <Erik.Leppo@tetratech.com>
Version: 1.0.5
Date: 2020-07-30
Depends: R (>= 3.2.0)
Imports: XLConnect
Suggests: knitr
SystemRequirements: Java (>= 8, <= 11)
License: GPL-3
Encoding: UTF-8
LazyData: TRUE
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-07-31 14:27:20 UTC; Erik.Leppo
Author: Jon Harcum [aut], Erik W. Leppo [aut, cre]
Repository: CRAN
Date/Publication: 2020-08-01 00:50:03 UTC

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Package terra updated to version 0.8-6 with previous version 0.8-5 dated 2020-07-28

Title: Spatial Data Analysis
Description: Methods for spatial data analysis, especially raster data. Methods allow for low-level data manipulation as well as high-level global, local, zonal, and focal computation. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/terra/> to get started. The package is similar to the 'raster' package; but 'terra' is simpler and faster.
Author: Robert J. Hijmans [cre, aut] (<https://orcid.org/0000-0001-5872-2872>), Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>), Karl Forner [ctb], Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>), Edzer Pebesma [ctb] (<https://orcid.org/0000-0001-8049-7069>)
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>

Diff between terra versions 0.8-5 dated 2020-07-28 and 0.8-6 dated 2020-07-31

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Package rRofex updated to version 2.0.3 with previous version 2.0.2 dated 2020-07-14

Title: Interface to 'Matba Rofex' Trading API
Description: Execute API calls to the 'Matba Rofex' <https://apihub.primary.com.ar> trading platform. Functionality includes accessing account data and current holdings, retrieving investment quotes, placing and canceling orders, and getting reference data for instruments.
Author: Augusto Hassel [aut, cre], Juan Francisco Gomez [ctb], Matba Rofex [cph]
Maintainer: Augusto Hassel <mpi-augusto@primary.com.ar>

Diff between rRofex versions 2.0.2 dated 2020-07-14 and 2.0.3 dated 2020-07-31

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Package NNS updated to version 0.5.4.3 with previous version 0.5.4.1 dated 2020-07-01

Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>

Diff between NNS versions 0.5.4.1 dated 2020-07-01 and 0.5.4.3 dated 2020-07-31

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Package MIMSunit updated to version 0.9.2 with previous version 0.9.1 dated 2020-05-20

Title: Algorithm to Compute Monitor Independent Movement Summary Unit (MIMS-Unit)
Description: The MIMS-unit algorithm is developed to compute Monitor Independent Movement Summary Unit, a measurement to summarize raw accelerometer data while ensuring harmonized results across different devices. It also includes scripts to reproduce results in the related publication (John, D., Tang. Q., Albinali, F. and Intille, S. (2019) <doi:10.1123/jmpb.2018-0068>).
Author: Qu Tang [aut, cre] (<https://orcid.org/0000-0001-5415-0205>), Dinesh John [aut], Stephen Intille [aut], mHealth Research Group [cph] (https://mhealthgroup.org)
Maintainer: Qu Tang <tang.q@northeastern.edu>

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Package fs updated to version 1.5.0 with previous version 1.4.2 dated 2020-06-30

Title: Cross-Platform File System Operations Based on 'libuv'
Description: A cross-platform interface to file system operations, built on top of the 'libuv' C library.
Author: Jim Hester [aut, cre], Hadley Wickham [aut], libuv project contributors [cph] (libuv library), Joyent, Inc. and other Node contributors [cph] (libuv library), RStudio [cph, fnd]
Maintainer: Jim Hester <james.f.hester@gmail.com>

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Package spocc updated to version 1.1.0 with previous version 1.0.8 dated 2020-02-11

Title: Interface to Species Occurrence Data Sources
Description: A programmatic interface to many species occurrence data sources, including Global Biodiversity Information Facility ('GBIF'), 'USGSs' Biodiversity Information Serving Our Nation ('BISON'), 'iNaturalist', Berkeley 'Ecoinformatics' Engine, 'eBird', Integrated Digitized 'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes functionality for retrieving species occurrence data, and combining those data.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Karthik Ram [ctb], Ted Hart [ctb], rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package medExtractR updated to version 0.2 with previous version 0.1 dated 2019-07-01

Title: Extraction of Medication Information from Clinical Text
Description: Function and support for medication and dosing information extraction from free-text clinical notes. Medication entities that can be extracted include drug name, strength, dose amount, dose, frequency, intake time, and time of last dose.
Author: Hannah Weeks [aut, cre], Cole Beck [aut] (<https://orcid.org/0000-0002-6849-6255>), Leena Choi [aut]
Maintainer: Hannah Weeks <hannah.l.weeks@vanderbilt.edu>

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Package baycn updated to version 1.2.0 with previous version 1.1.0 dated 2020-03-10

Title: Bayesian Inference for Causal Networks
Description: A Bayesian hybrid approach for inferring Directed Acyclic Graphs (DAGs) for continuous, discrete, and mixed data. The algorithm can use the graph inferred by another more efficient graph inference method as input; the input graph may contain false edges or undirected edges but can help reduce the search space to a more manageable size. A Bayesian Markov chain Monte Carlo algorithm is then used to infer the probability of direction and absence for the edges in the network. References: Martin and Fu (2019) <arXiv:1909.10678>.
Author: Evan A Martin [aut, cre], Audrey Qiuyan Fu [aut]
Maintainer: Evan A Martin <evanamartin@gmail.com>

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Package ropenblas updated to version 0.2.7 with previous version 0.2.6 dated 2020-05-23

Title: Download, Compile and Link 'OpenBLAS' Library with R
Description: The 'ropenblas' package (<https://prdm0.github.io/ropenblas/>) is useful for users of any 'GNU/Linux' distribution. It will be possible to download, compile and link the 'OpenBLAS' library (<https://www.openblas.net/>) with the R language, always by the same procedure, regardless of the 'GNU/Linux' distribution used. With the 'ropenblas' package it is possible to download, compile and link the latest version of the 'OpenBLAS' library even the repositories of the 'GNU/Linux' distribution used do not include the latest versions of 'OpenBLAS'. If of interest, older versions of the 'OpenBLAS' library may be considered. Linking R with an optimized version of 'BLAS' (<http://www.netlib.org/blas/>) may improve the computational performance of R code. The 'OpenBLAS' library is an optimized implementation of 'BLAS' that can be easily linked to R with the 'ropenblas' package.
Author: Pedro Rafael D. Marinho [aut, cre]
Maintainer: Pedro Rafael D. Marinho <pedro.rafael.marinho@gmail.com>

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Package Phase12Compare updated to version 1.5 with previous version 1.3 dated 2019-10-02

Title: Simulates SPSO and Efftox Phase 12 Trials with Correlated Outcomes
Description: Simulating and conducting four phase 12 clinical trials with correlated binary bivariate outcomes described. Uses the 'Efftox' (efficacy and toxicity tradeoff, <https://biostatistics.mdanderson.org/SoftwareDownload/SingleSoftware/Index/2>) and SPSO (Semi-Parametric Stochastic Ordering) models with Utility and Desirability based objective functions for dose finding.
Author: Andrew G Chapple
Maintainer: Andrew G Chapple <achapp@lsuhsc.edu>

Diff between Phase12Compare versions 1.3 dated 2019-10-02 and 1.5 dated 2020-07-31

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Package Distance updated to version 1.0.1 with previous version 1.0.0 dated 2020-01-31

Title: Distance Sampling Detection Function and Abundance Estimation
Description: A simple way of fitting detection functions to distance sampling data for both line and point transects. Adjustment term selection, left and right truncation as well as monotonicity constraints and binning are supported. Abundance and density estimates can also be calculated (via a Horvitz-Thompson-like estimator) if survey area information is provided.
Author: David Lawrence Miller
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>

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Package mrds updated to version 2.2.3 with previous version 2.2.2 dated 2020-05-12

Title: Mark-Recapture Distance Sampling
Description: Animal abundance estimation via conventional, multiple covariate and mark-recapture distance sampling (CDS/MCDS/MRDS). Detection function fitting is performed via maximum likelihood. Also included are diagnostics and plotting for fitted detection functions. Abundance estimation is via a Horvitz-Thompson-like estimator.
Author: Jeff Laake <jeff.laake@noaa.gov>, David Borchers <dlb@st-and.ac.uk>, Len Thomas <len.thomas@st-and.ac.uk>, David Miller <dave@ninepointeightone.net> and Jon Bishop
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>

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Package mnt updated to version 1.3 with previous version 1.2 dated 2020-04-25

Title: Affine Invariant Tests of Multivariate Normality
Description: Various affine invariant multivariate normality tests are provided. It is designed to accompany the survey article Ebner, B. and Henze, N. (2020) <arXiv:2004.07332> titled "Tests for multivariate normality -- a critical review with emphasis on weighted L^2-statistics". We implement new and time honoured L^2-type tests of multivariate normality, such as the Baringhaus-Henze-Epps-Pulley (BHEP) test, the Henze-Zirkler test, the test of Henze-Jiménes-Gamero, the test of Henze-Jiménes-Gamero-Meintanis, the test of Henze-Visage, the Dörr-Ebner-Henze test based on harmonic oscillator and the Dörr-Ebner-Henze test based on a double estimation in a PDE. Secondly, we include the measures of multivariate skewness and kurtosis by Mardia, Koziol, Malkovich and Afifi and Móri, Rohatgi and Székely, as well as the associated tests. Thirdly, we include the tests of multivariate normality by Cox and Small, the 'energy' test of Székely and Rizzo, the tests based on spherical harmonics by Manzotti and Quiroz and the test of Pudelko. All the functions and tests need the data to be a n x d matrix where n is the samplesize (number of rows) and d is the dimension (number of columns).
Author: Lucas Butsch [aut], Bruno Ebner [aut, cre], Jaco Visagie [ctb], Johann Siemens [ctb]
Maintainer: Bruno Ebner <bruno.ebner@kit.edu>

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Package AMR updated to version 1.3.0 with previous version 1.2.0 dated 2020-05-28

Title: Antimicrobial Resistance Analysis
Description: Functions to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods, like those defined by Leclercq et al. (2013) <doi:10.1111/j.1469-0691.2011.03703.x> and the Clinical and Laboratory Standards Institute (2014) <isbn: 1-56238-899-1>.
Author: Matthijs S. Berends [aut, cre] (<https://orcid.org/0000-0001-7620-1800>), Christian F. Luz [aut, ctb] (<https://orcid.org/0000-0001-5809-5995>), Alexander W. Friedrich [aut, ths] (<https://orcid.org/0000-0003-4881-038X>), Bhanu N. M. Sinha [aut, ths] (<https://orcid.org/0000-0003-1634-0010>), Casper J. Albers [aut, ths] (<https://orcid.org/0000-0002-9213-6743>), Corinna Glasner [aut, ths] (<https://orcid.org/0000-0003-1241-1328>), Judith M. Fonville [ctb], Erwin E. A. Hassing [ctb], Eric H. L. C. M. Hazenberg [ctb], Annick Lenglet [ctb], Bart C. Meijer [ctb], Sofia Ny [ctb], Dennis Souverein [ctb]
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>

Diff between AMR versions 1.2.0 dated 2020-05-28 and 1.3.0 dated 2020-07-31

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Package SqlRender updated to version 1.6.8 with previous version 1.6.6 dated 2020-05-19

Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into different SQL dialects. These dialects include 'Microsoft Sql Server', 'Oracle', 'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', and 'SQLite'.
Author: Martijn Schuemie [aut, cre], Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>

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Package lavaSearch2 updated to version 1.5.6 with previous version 1.5.5 dated 2020-03-18

Title: Tools for Model Specification in the Latent Variable Framework
Description: Tools for model specification in the latent variable framework (add-on to the 'lava' package). The package contains three main functionalities: Wald tests/F-tests with improved control of the type 1 error in small samples, adjustment for multiple comparisons when searching for local dependencies, and adjustment for multiple comparisons when doing inference for multiple latent variable models.
Author: Brice Ozenne [aut, cre] (<https://orcid.org/0000-0001-9694-2956>)
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>

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Package tramME updated to version 0.0.3 with previous version 0.0.2 dated 2020-04-07

Title: Transformation Models with Mixed Effects
Description: Likelihood-based estimation of mixed-effects transformation models using the Template Model Builder (TMB). The technical details of transformation models are given in Hothorn et al. (2018) <doi:10.1111/sjos.12291>. The random effects are assumed to be normally distributed on the scale of the transformation function, the marginal likelihood is evaluated using the Laplace approximation, and the gradients are calculated with automatic differentiation (AD).
Author: Balint Tamasi [aut, cre] (<https://orcid.org/0000-0002-2629-7362>), Torsten Hothorn [ctb] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Balint Tamasi <balint.tamasi@uzh.ch>

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Package raptr updated to version 0.1.7 with previous version 0.1.6 dated 2020-03-11

Title: Representative and Adequate Prioritization Toolkit in R
Description: Biodiversity is in crisis. The overarching aim of conservation is to preserve biodiversity patterns and processes. To this end, protected areas are established to buffer species and preserve biodiversity processes. But resources are limited and so protected areas must be cost-effective. This package contains tools to generate plans for protected areas (prioritizations), using spatially explicit targets for biodiversity patterns and processes. To obtain solutions in a feasible amount of time, this package uses the commercial 'Gurobi' software package (obtained from <http://www.gurobi.com/>). For more information on using this package, see Hanson et al. (2018) <doi:10.1111/2041-210X.12862>.
Author: Jeffrey O Hanson [aut, cre], Jonathan R Rhodes [aut], Hugh P Possingham [aut], Richard A Fuller [aut]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>

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Package modernVA updated to version 0.1.1 with previous version 0.1.0 dated 2020-07-18

Title: An Implementation of Two Modern Education-Based Value-Added Models
Description: Provides functions that fit two modern education-based value-added models. One of these models is the quantile value-added model. This model permits estimating a school's value-added based on specific quantiles of the post-test distribution. Estimating value-added based on quantiles of the post-test distribution provides a more complete picture of an education institution's contribution to learning for students of all abilities. See Page, G.L.; San Martín, E.; Orellana, J.; Gonzalez, J. (2017) <doi:10.1111/rssa.12195> for more details. The second model is a temporally dependent value-added model. This model takes into account the temporal dependence that may exist in school performance between two cohorts in one of two ways. The first is by modeling school random effects with a non-stationary AR(1) process. The second is by modeling school effects based on previous cohort's post-test performance. In addition to more efficiently estimating value-added, this model permits making statements about the persistence of a schools effectiveness. The standard value-added model is also an option.
Author: Garritt L. Page [aut, cre, cph], S. McKay Curtis [ctb, cph], Radford M. Neal [ctb, cph]
Maintainer: Garritt L. Page <page@stat.byu.edu>

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Package miic updated to version 1.4.2 with previous version 1.4.0 dated 2020-07-22

Title: Learning Causal or Non-Causal Graphical Models Using Information Theory
Description: We report an information-theoretic method which learns a large class of causal or non-causal graphical models from purely observational data, while including the effects of unobserved latent variables, commonly found in many datasets. Starting from a complete graph, the method iteratively removes dispensable edges, by uncovering significant information contributions from indirect paths, and assesses edge-specific confidences from randomization of available data. The remaining edges are then oriented based on the signature of causality in observational data. This approach can be applied on a wide range of datasets and provide new biological insights on regulatory networks from single cell expression data, genomic alterations during tumor development and co-evolving residues in protein structures. For more information you can refer to: Cabeli et al. PLoS Comp. Bio. 2020 <doi:10.1371/journal.pcbi.1007866>, Verny et al. PLoS Comp. Bio. 2017 <doi:10.1371/journal.pcbi.1005662>.
Author: Vincent Cabeli [aut, cre], Honghao Li [aut], Marcel Ribeiro Dantas [aut], Nadir Sella [aut], Louis Verny [aut], Severine Affeldt [aut], Hervé Isambert [aut]
Maintainer: Vincent Cabeli <vincent.cabeli@curie.fr>

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Package libgeos updated to version 3.8.1-3 with previous version 3.8.1-2 dated 2020-07-21

Title: Open Source Geometry Engine ('GEOS') C API
Description: Provides the Open Source Geometry Engine ('GEOS') as a C API that can be used to write high-performance C and C++ geometry operations using R as an interface. Headers are provided to make linking to and using these functions from C++ code as easy and as safe as possible. This package contains an internal copy of the 'GEOS' library to guarantee the best possible consistency on multiple platforms.
Author: Dewey Dunnington [aut, cre] (<https://orcid.org/0000-0002-9415-4582>), GEOS authors [aut], Martin Davis [ctb, cph], Benjamin Campbell [ctb, cph], Tomasz Sowa [ctb, cph], Christian Kaiser [ctb, cph], David Skea [ctb, cph], Daniel Baston [ctb, cph], Sandro Santilli [ctb, cph], Mateusz Loskot [ctb, cph], Paul Ramsey [ctb, cph], Olivier Devillers [ctb, cph], Sean Gillies [ctb, cph], Mika Heiskanen [ctb, cph], Safe Software Inc. [cph], Refractions Research Inc. [cph], Vivid Solutions Inc. [cph]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>

Diff between libgeos versions 3.8.1-2 dated 2020-07-21 and 3.8.1-3 dated 2020-07-31

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More information about libgeos at CRAN
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Package brms updated to version 2.13.5 with previous version 2.13.3 dated 2020-07-13

Title: Bayesian Regression Models using 'Stan'
Description: Fit Bayesian generalized (non-)linear multivariate multilevel models using 'Stan' for full Bayesian inference. A wide range of distributions and link functions are supported, allowing users to fit -- among others -- linear, robust linear, count data, survival, response times, ordinal, zero-inflated, hurdle, and even self-defined mixture models all in a multilevel context. Further modeling options include non-linear and smooth terms, auto-correlation structures, censored data, meta-analytic standard errors, and quite a few more. In addition, all parameters of the response distribution can be predicted in order to perform distributional regression. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their beliefs. Model fit can easily be assessed and compared with posterior predictive checks and leave-one-out cross-validation. References: Bürkner (2017) <doi:10.18637/jss.v080.i01>; Bürkner (2018) <doi:10.32614/RJ-2018-017>; Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.
Author: Paul-Christian Bürkner [aut, cre], Jonah Gabry [ctb]
Maintainer: Paul-Christian Bürkner <paul.buerkner@gmail.com>

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Package tidyr updated to version 1.1.1 with previous version 1.1.0 dated 2020-05-20

Title: Tidy Messy Data
Description: Tools to help to create tidy data, where each column is a variable, each row is an observation, and each cell contains a single value. 'tidyr' contains tools for changing the shape (pivoting) and hierarchy (nesting and 'unnesting') of a dataset, turning deeply nested lists into rectangular data frames ('rectangling'), and extracting values out of string columns. It also includes tools for working with missing values (both implicit and explicit).
Author: Hadley Wickham [aut, cre], Lionel Henry [aut], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between tidyr versions 1.1.0 dated 2020-05-20 and 1.1.1 dated 2020-07-31

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Package dplyr updated to version 1.0.1 with previous version 1.0.0 dated 2020-05-29

Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects, both in memory and out of memory.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>), Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>), Lionel Henry [aut], Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>), RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between dplyr versions 1.0.0 dated 2020-05-29 and 1.0.1 dated 2020-07-31

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Package permubiome updated to version 1.3.1 with previous version 1.3 dated 2019-12-10

Title: A Permutation Based Test for Biomarker Discovery in Microbiome Data
Description: The permubiome R package was created to perform a permutation-based non-parametric analysis on microbiome data for biomarker discovery aims. This test executes thousands of comparisons in a pairwise manner, after a random shuffling of data into the different groups of study with a prior selection of the microbiome features with the largest variation among groups. Previous to the permutation test itself, data can be normalized according to different methods proposed to handle microbiome data ('proportions' or 'Anders'). The median-based differences between groups resulting from the multiple simulations are fitted to a normal distribution with the aim to calculate their significance. A multiple testing correction based on Benjamini-Hochberg method (fdr) is finally applied to extract the differentially presented features between groups of your dataset. LATEST UPDATES: v1.1 and olders incorporates function to parse COLUMN format; v1.2 and olders incorporates -optimize- function to maximize evaluation of features with largest inter-class variation; v1.3 and olders includes the -size.effect- function to perform estimation statistics using the bootstrap-coupled approach implemented in the 'dabestr' (>=0.3.0) R package.
Author: Alfonso Benitez-Paez
Maintainer: Alfonso Benitez-Paez <alfbenpa@gmail.com>

Diff between permubiome versions 1.3 dated 2019-12-10 and 1.3.1 dated 2020-07-31

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Package maxLik updated to version 1.4-0 with previous version 1.3-8 dated 2020-01-10

Title: Maximum Likelihood Estimation and Related Tools
Description: Functions for Maximum Likelihood (ML) estimation, non-linear optimization, and related tools. It includes a unified way to call different optimizers, and classes and methods to handle the results from the Maximum Likelihood viewpoint. It also includes a number of convenience tools for testing and developing your own models.
Author: Ott Toomet <otoomet@gmail.com>, Arne Henningsen <arne.henningsen@gmail.com>, with contributions from Spencer Graves and Yves Croissant
Maintainer: Ott Toomet <otoomet@gmail.com>

Diff between maxLik versions 1.3-8 dated 2020-01-10 and 1.4-0 dated 2020-07-31

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Package lavaan updated to version 0.6-7 with previous version 0.6-6 dated 2020-05-13

Title: Latent Variable Analysis
Description: Fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models.
Author: Yves Rosseel [aut, cre] (<https://orcid.org/0000-0002-4129-4477>), Terrence D. Jorgensen [aut] (<https://orcid.org/0000-0001-5111-6773>), Nicholas Rockwood [aut] (<https://orcid.org/0000-0001-5931-183X>), Daniel Oberski [ctb], Jarrett Byrnes [ctb], Leonard Vanbrabant [ctb], Victoria Savalei [ctb], Ed Merkle [ctb], Michael Hallquist [ctb], Mijke Rhemtulla [ctb], Myrsini Katsikatsou [ctb], Mariska Barendse [ctb], Florian Scharf [ctb]
Maintainer: Yves Rosseel <Yves.Rosseel@UGent.be>

Diff between lavaan versions 0.6-6 dated 2020-05-13 and 0.6-7 dated 2020-07-31

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Package TmCalculator updated to version 1.0.1 with previous version 1.0.0 dated 2019-02-11

Title: Melting Temperature of Nucleic Acid Sequences
Description: This tool is extended from methods in Bio.SeqUtils.MeltingTemp of python. The melting temperature of nucleic acid sequences can be calculated in three method, the Wallace rule (Thein & Wallace (1986) <doi:10.1016/S0140-6736(86)90739-7>), empirical formulas based on G and C content (Marmur J. (1962) <doi:10.1016/S0022-2836(62)80066-7>, Schildkraut C. (2010) <doi:10.1002/bip.360030207>, Wetmur J G (1991) <doi:10.3109/10409239109114069>, Untergasser,A. (2012) <doi:10.1093/nar/gks596>, von Ahsen N (2001) <doi:10.1093/clinchem/47.11.1956>) and nearest neighbor thermodynamics (Breslauer K J (1986) <doi:10.1073/pnas.83.11.3746>, Sugimoto N (1996) <doi:10.1093/nar/24.22.4501>, Allawi H (1998) <doi:10.1093/nar/26.11.2694>, SantaLucia J (2004) <doi:10.1146/annurev.biophys.32.110601.141800>, Freier S (1986) <doi:10.1073/pnas.83.24.9373>, Xia T (1998) <doi:10.1021/bi9809425>, Chen JL (2012) <doi:10.1021/bi3002709>, Bommarito S (2000) <doi:10.1093/nar/28.9.1929>, Turner D H (2010) <doi:10.1093/nar/gkp892>, Sugimoto N (1995) <doi:10.1016/S0048-9697(98)00088-6>, Allawi H T (1997) <doi:10.1021/bi962590c>, Santalucia N (2005) <doi:10.1093/nar/gki918>), and it can also be corrected with salt ions and chemical compound (SantaLucia J (1996) <doi:10.1021/bi951907q>, SantaLucia J(1998) <doi:10.1073/pnas.95.4.1460>, Owczarzy R (2004) <doi:10.1021/bi034621r>, Owczarzy R (2008) <doi:10.1021/bi702363u>).
Author: Junhui Li
Maintainer: Junhui Li <junhuili@cau.edu.cn>

Diff between TmCalculator versions 1.0.0 dated 2019-02-11 and 1.0.1 dated 2020-07-31

 TmCalculator-1.0.0/TmCalculator/R/TmCalculator-internal.R   |only
 TmCalculator-1.0.1/TmCalculator/DESCRIPTION                 |   10 +++++-----
 TmCalculator-1.0.1/TmCalculator/MD5                         |    7 +++----
 TmCalculator-1.0.1/TmCalculator/R/salt_correction.R         |   11 +++++++----
 TmCalculator-1.0.1/TmCalculator/man/TmCalculator-package.Rd |    4 ++--
 5 files changed, 17 insertions(+), 15 deletions(-)

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